mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | CP000731 | 81 | N→G | 100% | intergenic (–/‑151) | – / → repA | –/replication protein A |
| JC | CP000731 | 6,552 | +28 bp | 100% | intergenic (+1069/‑419) | cadX → / → USA300HOU_pUSA300HOUMR0010 | cadmium efflux regulator/MarR family transcriptional regulator |
| RA | CP000731 | 25,663 | Δ1 bp | 100% | coding (316/333 nt) | USA300HOU_pUSA300HOUMR0031 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 37,589 | G→T | 8.0% | intergenic (+613/‑224) | USA300HOU_RS14915 → / → ugpQ_1 | hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic |
| RA | USA300TCH1516_ALE | 94,164 | G→A | 8.7% | Q5Q (CAG→CAA) | gloC_2 → | Hydroxyacylglutathione hydrolase GloC |
| RA | USA300TCH1516_ALE | 108,148 | A→G | 11.8% | K1037R (AAA→AGA) | recD → | RecBCD enzyme subunit RecD |
| RA | USA300TCH1516_ALE | 110,651 | C→T | 10.6% | D170D (GAC→GAT) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 110,660 | T→A | 12.3% | I173I (ATT→ATA) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 23.8% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 25.0% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 187,439 | G→T | 8.0% | A81S (GCA→TCA) | gnu → | N‑acetyl‑alpha‑D‑glucosaminyl‑diphospho‑ditrans, octacis‑undecaprenol 4‑epimerase |
| RA | USA300TCH1516_ALE | 189,365 | A→G | 16.7% | Y409C (TAT→TGT) | wecC → | UDP‑N‑acetyl‑D‑mannosamine dehydrogenase |
| RA | USA300TCH1516_ALE | 264,793 | T→C | 8.2% | L319L (CTT→CTC) | ugpQ_2 → | Glycerophosphodiester phosphodiesterase, cytoplasmic |
| RA | USA300TCH1516_ALE | 265,956 | T→C | 11.4% | I51M (ATA→ATG) | scn_1 ← | Staphylococcal complement inhibitor |
| RA | USA300TCH1516_ALE | 387,871 | G→T | 8.3% | S175I (AGT→ATT) | mepA → | Multidrug export protein MepA |
| RA | USA300TCH1516_ALE | 414,995 | T→C | 7.0% | I25T (ATA→ACA) | spo0C → | Chromosome‑partitioning protein Spo0J |
| RA | USA300TCH1516_ALE | 494,590 | A→G | 9.3% | I138T (ATT→ACT) | USA300HOU_RS02360 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 48.2% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 591,934 | Δ1 bp | 5.3% | coding (2150/3624 nt) | rpoC → | DNA‑directed RNA polymerase subunit beta' |
| RA | USA300TCH1516_ALE | 622,019 | T→C | 9.7% | L861S (TTG→TCG) | sdrE → | Serine‑aspartate repeat‑containing protein E |
| RA | USA300TCH1516_ALE | 866,495 | G→A | 12.4% | C346Y (TGT→TAT) | rnr → | Ribonuclease R |
| RA | USA300TCH1516_ALE | 915,857 | C→T | 9.0% | A5V (GCA→GTA) | sufB_2 → | FeS cluster assembly protein SufB |
| RA | USA300TCH1516_ALE | 966,439 | A→G | 7.1% | S169S (TCA→TCG) | addA → | ATP‑dependent helicase/nuclease subunit A |
| RA | USA300TCH1516_ALE | 984,788 | C→T | 10.0% | A50T (GCT→ACT) | USA300HOU_RS04870 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 989,442 | C→A | 10.0% | Q141K (CAG→AAG) | oppC → | Oligopeptide transport system permease protein OppC |
| RA | USA300TCH1516_ALE | 995,747 | C→T | 9.9% | intergenic (+24/‑27) | appA → / → oppD_3 | Oligopeptide‑binding protein AppA/Oligopeptide transport ATP‑binding protein OppD |
| RA | USA300TCH1516_ALE | 1,091,403 | T→C | 12.0% | S378P (TCT→CCT) | rlmI → | Ribosomal RNA large subunit methyltransferase I |
| RA | USA300TCH1516_ALE | 1,181,141 | T→C | 7.9% | intergenic (‑145/‑104) | USA300HOU_RS05880 ← / → USA300HOU_RS05885 | hypothetical protein/hypothetical protein |
| RA | USA300TCH1516_ALE | 1,202,470 | G→A | 10.0% | V483I (GTT→ATT) | ileS → | Isoleucine‑‑tRNA ligase |
| RA | USA300TCH1516_ALE | 1,276,099 | T→A | 8.5% | T146T (ACT→ACA) | tsf → | Elongation factor Ts |
| RA | USA300TCH1516_ALE | 1,291,644 | G→A | 12.6% | G439D (GGT→GAT) | infB → | Translation initiation factor IF‑2 |
| RA | USA300TCH1516_ALE | 1,414,715 | T→C | 15.2% | L165S (TTG→TCG) | yitU_2 → | 5‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase YitU |
| RA | USA300TCH1516_ALE | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD_4 ← | Oligopeptide transport ATP‑binding protein OppD |
| RA | USA300TCH1516_ALE | 1,513,930 | A→T | 100% | L413F (TTA→TTT) | USA300HOU_RS07375 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,540,760 | A→G | 10.3% | F146S (TTC→TCC) | hepT ← | Heptaprenyl diphosphate synthase component 2 |
| RA | USA300TCH1516_ALE | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | ypdF ← | Aminopeptidase YpdF |
| RA | USA300TCH1516_ALE | 1,672,327 | A→G | 16.3% | V222V (GTT→GTC) | sigA ← | RNA polymerase sigma factor SigA |
| RA | USA300TCH1516_ALE | 1,732,905 | T→A | 10.8% | intergenic (+91/+146) | limB_2 → / ← USA300HOU_RS08645 | Limonene 1,2‑monooxygenase/hypothetical protein |
| RA | USA300TCH1516_ALE | 1,776,059 | A→G | 6.8% | D155D (GAT→GAC) | clpX ← | ATP‑dependent Clp protease ATP‑binding subunit ClpX |
| RA | USA300TCH1516_ALE | 1,797,152 | G→A | 18.4% | S213S (TCC→TCT) | phoR ← | Alkaline phosphatase synthesis sensor protein PhoR |
| RA | USA300TCH1516_ALE | 1,842,707 | T→C | 6.9% | I204V (ATT→GTT) | tyrS ← | Tyrosine‑‑tRNA ligase |
| RA | USA300TCH1516_ALE | 1,980,512 | G→T | 6.5% | Q83K (CAA→AAA) | USA300HOU_RS09865 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
| RA | USA300TCH1516_ALE | 2,018,582 | T→A | 9.8% | K113* (AAA→TAA) | mgt ← | Monofunctional glycosyltransferase |
| RA | USA300TCH1516_ALE | 2,028,124 | G→A | 34.2% | P174L (CCG→CTG) | USA300HOU_RS10230 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,057,798 | C→A | 5.5% | R165L (CGA→CTA) | USA300HOU_RS10380 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,094,261 | A→G | 14.3% | T553T (ACT→ACC) | USA300HOU_RS10605 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,101,143 | A→G | 5.5% | V268A (GTA→GCA) | mepM_1 ← | Murein DD‑endopeptidase MepM |
| RA | USA300TCH1516_ALE | 2,128,065 | A→G | 18.2% | K273E (AAA→GAA) | xerC_2 → | Tyrosine recombinase XerC |
| RA | USA300TCH1516_ALE | 2,279,705 | G→A | 100% | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,358,670 | T→C | 10.0% | K83R (AAA→AGA) | rpoA_1 ← | DNA‑directed RNA polymerase subunit alpha |
| RA | USA300TCH1516_ALE | 2,372,751 | A→T | 23.1% | L342* (TTA→TAA) | pbuG ← | Guanine/hypoxanthine permease PbuG |
| RA | USA300TCH1516_ALE | 2,373,531 | G→T | 13.6% | A82E (GCG→GAG) | pbuG ← | Guanine/hypoxanthine permease PbuG |
| RA | USA300TCH1516_ALE | 2,373,714 | C→T | 33.3% | G21D (GGT→GAT) | pbuG ← | Guanine/hypoxanthine permease PbuG |
| RA | USA300TCH1516_ALE | 2,405,833 | A→G | 9.3% | E74G (GAA→GGA) | ureA → | Urease subunit gamma |
| RA | USA300TCH1516_ALE | 2,425,673 | A→G | 11.6% | F837L (TTT→CTT) | USA300HOU_RS12500 ← | Putative formate dehydrogenase |
| RA | USA300TCH1516_ALE | 2,451,070 | T→C | 9.8% | K116K (AAA→AAG) | hutU ← | Urocanate hydratase |
| RA | USA300TCH1516_ALE | 2,462,758 | G→A | 25.0% | A70T (GCA→ACA) | USA300HOU_RS12680 → | Putative 3‑methyladenine DNA glycosylase |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,532,665 | G→T | 10.3% | G138C (GGT→TGT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,568,885 | T→A | 9.3% | L245* (TTA→TAA) | pbpX_2 → | Putative penicillin‑binding protein PbpX |
| RA | USA300TCH1516_ALE | 2,615,078 | A→G | 17.0% | G919G (GGT→GGC) | radD ← | Putative DNA repair helicase RadD |
| RA | USA300TCH1516_ALE | 2,638,727 | C→T | 8.7% | D240N (GAT→AAT) | xylB ← | Xylulose kinase |
| RA | USA300TCH1516_ALE | 2,656,802 | A→T | 6.4% | S72R (AGT→AGA) | mhqR ← | HTH‑type transcriptional regulator MhqR |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000731 | = 64 | 44 (0.400) | 3 (0.040) +33 bp |
3/194 | NT | 15.5% | intergenic (–/‑168) | –/repA | –/replication protein A |
| ? | CP000731 | = 27041 | 0 (0.000) | intergenic (‑194/–) | USA300HOU_pUSA300HOUMR0033/– | partitioning protein/– | |||||
| * | ? | USA300TCH1516_ALE | 512620 = | 39 (1.000) | 31 (1.220) +45 bp |
20/170 | NT | 51.4% | intergenic (+688/‑6075) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| ? | USA300TCH1516_ALE | 2176447 = | 51 (1.310) | intergenic (+209/+5086) | ilvA/USA300TCH1516_02069 | L‑threonine dehydratase biosynthetic IlvA/tRNA‑Gly | |||||
| * | ? | USA300TCH1516_ALE | 895785 = | 48 (1.230) | 9 (0.270) | 8/226 | NT | 22.0% | coding (806/822 nt) | metQ_2 | Methionine‑binding lipoprotein MetQ |
| ? | USA300TCH1516_ALE | = 909740 | 22 (0.650) | intergenic (‑663/‑371) | USA300HOU_RS04500/csbD_1 | hypothetical protein/Stress response protein CsbD | |||||
| * | ? | USA300TCH1516_ALE | 2085296 = | 26 (0.670) | 7 (0.200) | 5/232 | NT | 18.1% | coding (173/201 nt) | hlb_1 | Phospholipase C |
| ? | USA300TCH1516_ALE | = 2128343 | 40 (1.150) | coding (1/825 nt) | hlb_2 | Phospholipase C | |||||